I have bind 9 installed, will this conflict with the workings of the dyndns site? With the DNS etc? i dont know how it can because the control panel works, i have tested it on a different internet connection and it works fine. it seems only the web sites arent working.

also in the /etc/hosts - do i have to fill in every domain under the ip i am using?

the domain that i have is the domain that i`m using for ispconfig server, ie:
under management and settings i have my domain name as the host and domain. are you asking me to create a site with this same domain name?

i have another domain that i created with dyndns and i have tried to create a site with this domain, and it didnt work.

or do i need to create a site with the first domain that is also my isp servers domain?

You can use whatever domain you like to create a web site, but make sure that its DNS records are pointing to your server.
Regarding the IP address that you have to choose for the web site in ISPConfig: it must be one of the IP addresses that you see in the output of